{"id":23057372,"url":"https://github.com/applicativesystem/go-diamond-tags","last_synced_at":"2025-04-03T06:12:46.053Z","repository":{"id":262142606,"uuid":"867039097","full_name":"applicativesystem/go-diamond-tags","owner":"applicativesystem","description":"metacoverage estimation and tags generation from diamond aligner","archived":false,"fork":false,"pushed_at":"2024-10-16T05:36:51.000Z","size":5925,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-12-16T02:12:08.757Z","etag":null,"topics":["genome-analysis","genome-analysis-annotation","genome-annotation","metagenome-annotation","metagenome-assembled-genomes","metagenome-assembly"],"latest_commit_sha":null,"homepage":"","language":"Go","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/applicativesystem.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-10-03T10:44:36.000Z","updated_at":"2024-10-16T05:36:54.000Z","dependencies_parsed_at":"2024-11-10T20:18:16.257Z","dependency_job_id":null,"html_url":"https://github.com/applicativesystem/go-diamond-tags","commit_stats":null,"previous_names":["applicativesystem/go-diamond-tags"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fgo-diamond-tags","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fgo-diamond-tags/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fgo-diamond-tags/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fgo-diamond-tags/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/applicativesystem","download_url":"https://codeload.github.com/applicativesystem/go-diamond-tags/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":237863998,"owners_count":19378257,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["genome-analysis","genome-analysis-annotation","genome-annotation","metagenome-annotation","metagenome-assembled-genomes","metagenome-assembly"],"created_at":"2024-12-16T02:12:06.096Z","updated_at":"2025-02-08T19:45:03.633Z","avatar_url":"https://github.com/applicativesystem.png","language":"Go","funding_links":[],"categories":[],"sub_categories":[],"readme":"# go-diamond-tags\n\n- a subfunction for the diamond-aligner and estimating the hsp coverage\n- this is also integratd into the go-mapper-diamond\n- you can use this as a separate if you have already aligned reads to the protein.\n- when you have a metagenome and you want to generate the annotation tags using the bacterial genome proteins.\n- when you have MAGS and you want to generate the specific mags to protein alignment.  \n- same goes for other species also. \n- your pacbio reads should be a linear fasta, which is the way the pacbio reads usually comes.\n- Incase of the other fasta sequences such as genomes or others, remember to run the awk utility to linearize it. This is faster than implementing a loop iteration. \n\n```\nawk '/^\u003e/ {printf(\"\\n%s\\n\",$0);next; } { printf(\"%s\",$0);}  \\\n                         END {printf(\"\\n\");}' inputfasta \u003e output.fasta\n```\n\n```\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-tags ±main⚡ » \\\ngo run main.go -h\nAnalyzer for the diamond aligner and pacbio reads for hints\n\nUsage:\n  analyze [command]\n\nAvailable Commands:\n  alignment\n  completion  Generate the autocompletion script for the specified shell\n  help        Help about any command\n\nFlags:\n  -h, --help   help for analyze\n\nUse \"analyze [command] --help\" for more information about a command.\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-tags ±main⚡ » \\\ngo run main.go alignment -h\nAnalyzes the hsp from the diamond read to protein alignment\n\nUsage:\n  analyze alignment [flags]\n\nFlags:\n  -a, --alignmentfile string   alignment (default \"alignment file to be analyzed\")\n  -h, --help                   help for alignment\n  -p, --pacbioreads string     pacbio file (default \"pacbio reads file\")\n\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-tags ±main⚡ » \\\ngo run main.go alignment -a matches.tsv -p ./samplefiles/pacbioreads.fasta\nchr10:66478458-66505490 1.0061776347427218\nchr10:66478458-66505490 0.9026005252839123\nchr11:66478458-66505490 0.8952021603225687\nchr11:66478458-66505490 1.0875596493175008\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-tags ±main⚡ » \\\ncat coveragestimation.txt\nchr10:66478458-66505490        1.0061776347427218\nchr10:66478458-66505490        0.9026005252839123\nchr11:66478458-66505490        0.8952021603225687\nchr11:66478458-66505490        1.0875596493175008\n\n```\nGaurav Sablok\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapplicativesystem%2Fgo-diamond-tags","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fapplicativesystem%2Fgo-diamond-tags","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapplicativesystem%2Fgo-diamond-tags/lists"}